CAM Provider KG

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Causal Activity Model (CAM) - Adverse Outcome Pathway (AOP) Knowledge Provider (KP) Service

Brief Overview

Homepage URL: https://robokop.renci.org/api-docs/docs/automat/cam-provider-kg

Description: CAM - AOP KP is a service that provides access to causal activity models as part of Translator. Causal activity models are small knowledge graphs that model context-specific interactions between instances of entities defined in bio-ontologies.

Example edge interpretation: CAM - AOP KP shows that the ubiquitin-protein transferase activity of NEDD4 is part of a ubiquitin-dependent catabolic process that negatively regulates RNA polymerase II activity in the nucleus.

Data source: CAM - AOP KP exposes causal activity models curated by the Gene Ontology Consortium, as well as models translated from the Reactome database.

Key methodologic metrics: CAM - AOP KP models are described in the Web Ontology Language (OWL), allowing logical consistency checking and deduction of inferred statements.

Regulatory requirement(s) and/or licensing restriction(s): Service is compliant with all federal and institutional regulations.

Note that CAM KP is being extended to support causal data on Adverse Outcome Pathways (AOPs), derived from the (AOP-wiki)[https://aopwiki.org/]. This work is under development.

Detailed Description

Description- CAMs (Causal Activity Models) are small knowledge graphs built using the Web Ontology Language (OWL). The CAM database combines many CAM graphs along with a large merged bio-ontology containing the full vocabulary of concepts referenced within the individual CAMs. Each CAM describes an instantiation of some of those concepts in a particular context, modeling the interactions between those instances as an interlinked representation of a complex biological or environmental process.

The CAM/AOP KP is a product of the Exposures Provider team.

Click here to view the CAM-KP GitHub repo.

• Technical User Guide to CAM-KP- Anyone can query the database by posting the query here: CAM-KP API (/cam-kp/1.4/query endpoint). Click here for some example queries.

• Modes of Access- CAM-KP API v0.1, SmartAPI Registry

  • CAM-AOP Service GUI
  • CAM-KP API (/cam-kp/1.4/query)
  • SmartAPI Registration

• Issue Management- Anyone can create new issues by clicking on "New issue" button on the issues page of this repository.

• Building- The CAM-KP API project is written in Scala. The build tool used to execute numerous development tasks is the Scala Build Tool (SBT).

  Compiling

  cam-kp-api$ sbt compile
  cam-kp-api$ sbt test:compile
  cam-kp-api$ sbt it:compile
  

  Deploying to a local Docker container

  cam-kp-api$ sbt docker:stage docker:publishLocal
  

  Running from a local Docker container

  cam-kp-api$ docker run -p 8080:8080 -it renciorg/cam-kp-api:0.1
  

  Note that the version used in these examples may not reflect the latest build version.

Use Cases

See the user guide above.

Knowledge Sources Accessed

• Gene Ontology GO-CAM knowledgebase
• Reactome pathway knowledgebase
• pathways2GO

Source Code

• CAM-KP TRAPI API
• CAM ingest/processing pipeline

Team Contact:

Jim Balhoff